Taking the Ultramar ferry from Puerto Juarez is still the most economical, but since they have doubled the prices recently they are no longer the hands-down best choice. But you can decide if the convenience and transportation cost is worth it depending on where you're starting from and how many people you have in your group.
Isla Mujeres From the AirportThe cheapest way to get from the airport to Isla Mujeres depends on how many people you have. If you have more than a few, then book a private van. Because it's more expensive to get to the hotel zone, there's no question that Puerto Juarez is the best place to get the ferry if you're coming from the airport.
Private Shuttle ($29 up to 8 people)You're really not going to get a shared shuttle (not currently available anyway with COVID concerns) to Puerto Juarez like you would to the Hotel Zone. A private van costs $29 OW or $50 RT. BOOK AHEAD and order a some cold drinks for the ride. Read a little more about CUN airport shuttles here: Cheapest Transportation from Cancún Airport.
ADO Bus then Taxi ($10)Also conveniently waiting outside the airport terminal, is the ADO bus. A nice coach that will take you to the ADO bus terminal downtown for around $5 USD per person. From there, you can get a taxi for around 100 MXN ($5) to Gran Puerto / Puerto Juárez.
ADO Bus then Colectivo ($5.50)Take the ADO bus to the bus terminal downtown. At the bus station, ask where to get a colectivo to Puerto Juarez. It will either be just across Ave Uxmal or across Ave Tulum. Cross the street and hail a colecitvo van with Pto. Juarez across the top of the windshield. Shove yourself in the van in any slightly open space, bag on lap, and enjoy the local experience. The ride will cost you $.50. If you have anything other than a carry-on, and trust me it's even difficult with just that, you won't have room. They cram as many people as they can into the hot van and it's probably pretty full by the time it gets to the bus terminal.
Isla Mujeres From the Hotel Zone
Via Puerto Juarez by BusFrom the Hotel Zone, some public bus R1 are marked as going to Puerto Juarez, but it's not every R1 and quite frankly they don't run very often. You probably won't be able to see the Pto Juarez, sign in time before the bus drives by you, so just flag down the R1 anyway, and if it doesn't say Puerto Juarez (or Gran Puerto) on it, then wave the driver on. When you hop on the bus, tell the driver you are going to Gran Puerto. If you get tired of waiting for the R1 going to Pto Juarez, just take any R1 or R2 downtown, get off as soon as you're in the city, and take a taxi to the port.
Via Puerto Juarez by TaxiYou can also take a taxi if you don't have time to wait for the bus. But, depending on the size of your group, by the time you pay $10+ for a taxi to Puerto Juarez, you might just as well spend less to go to one of the 3 closer ports within the Hotel Zone (even though you'll pay more for the ferry) and go from there. Hopefully you didn't have too many piña coladas at the pool the night before, because you'll need to put on your math brain here.
Via Hotel Zone Ports by Bus or TaxiWithin the hotel zone, just hop on the frequent local bus for $.50. The R1 and R2 buses will pass along the strip going north toward the city and past the 3 ports that are along then north edge of the hotel zone in this order: Playa Caracol, Playa Tortugas, El Embarcadero. Just tell them at which port you'd like to get off, likely Playa Caracol since that one is first. Larger group? You can get a taxi but the bus is cheaper.
Isla Mujeres From Downtown CancúnIf you are in the city, you can take a colectivo or taxi to Puerto Juarez for very little. A taxi (which you can really hail from anywhere) will cost around $5 from the ADO bus terminal. Colectivos are only $.50 if you don't have much luggage and don't mind being crammed in a van and waiting until it fills up to leave. If I remember right, you can get them on the north east corner of Bnampak and Kukulcan, and you can also hail one from across the street from the ADO bus terminal (ask at the terminal where to wait exactly).
On the IslandOnce you arrive on the island, you can easily walk to Playa Norte from the ferry dock or you can take a taxi for 40 pesos. It's about 1/4 mile.
FROM Isla Mujeres to the Airport or Hotel ZoneOnce again, this depends on the size of your group. With enough people, it's worth it to get a cab or pre-arranged shuttle. There are plenty of taxis and shuttles inside the port parking lot. IGNORE THEM. They will try to rip you off like it's nobody's business. Walk outside and across the small street where you can catch a taxi or a bus for a fraction of the cost. If you have enough people, you can also book a shuttle ahead of time to meet you at the ferry.
To the AirportTake a taxi or shuttle as stated above. For the taxi, do your best bargaining and see if you can get a taxi for 300 MXN / $15. In fact, just sort of state it like you are confirming the price, not like you are haggling. "300 aeropuerto?" and watch the guy cringe who followed you from across the street trying to charge you 4 times that amount.
I suppose you could always do the reverse route, too by taking a taxi or coletivo to the ADO bus terminal, and getting the ADO airport bus from there. It depends on how much time you have.