Thank you to everyone who helped me narrow down my choices. We are down to two, Isla Mujeres and Puerto Morelos. My understanding from various travel boards - and please correct me if I'm wrong! - is that IM is more isolated, has better beaches and better lodging and we move around on golf carts. PM is less isolated (for ruins and cenotes), has better food, has beaches that can be rocky and/or seaweed-y but has better snorkeling. Does that sound about right? We are having a very hard time choosing between these two locations. Which would you pick and why? Also, if we do stay in Puerto Morelos, what are the nicest beaches? We will most likely stay in a small hotel or Air B&B, not at a large resort. Thanks again. I'd be lost without you guys.

I love them both and have stayed in both places 5 times or more. If you have enough time, split your stay. Isla Mujeres you get to via a ferry from Puerto Juarez, ferry takes 20 minutes and runs every 30 minutes until 8:30, Puerto Morelos (note spelling) is a 20 minute drive south of Cancun. On Isla we usually only rent a golf cart for one day and walk or take taxis everywhere else. You won't need a cart the whole time unless you are staying south or in San Bajo (not a good idea) unless you want one.
Both have good food, Isla has over 100+ restaurants on a 5 mile long island. You will not starve.

We stayed up in the north beach area in IM at Na Balam-it was really lovely. We liked that area because you are still walking distance to downtown but away from most of noise etc. We have also heard good things about Ixchel Beach Hotel but it is much larger I think and more "hotel-like"

https://www.ixchelbeachhotel.com/default-en.html

Isla Mujeres Beachfront Hotels & Resorts at Playa Norte | Hotel Na Balam Isla Mujeres Cancun Mexico

Puerto Morelos's beach is gorgeous, wide and rock free as you get a bit north of the docks downtown. You can walk to pretty much every restaurant there. Not a ton of hotels per se, but lots and lots of reasonably priced vacation rentals.

You can split your stay, the ferry to IM takes like 20min approx. At IM you will find beautiful beaches, but near PM there are more places to visit.