I am on the Pacific coast of Mexico, so I can't advise on where the best place to clear in is on the Carib side, but I will advise that you apply for a T.I.P. (Temp
Import Permit) for you
boat before you leave the US. This article explains what it is and why you need it and includes a link to apply for one. You can wait and apply for one when you get there, but it adds a lot of hassle and time to the clearance process.
https://www.clubcruceros.net/CruisingBaja/TIP.html
Note that the TIP is good for 10 years and you can enter and leave Mexico multiple times during that period with the same TIP. However, if you sell your boat you must cancel the TIP or the new owner will have difficulties if they ever try to go to Mexico (the TIP while attached to the vessel/vehicle does not transfer to the new owner).
Oh, also - there is a
rule about
fishing in Mexico which says any vessel which has
fishing gear on board (whether you use it or not) must have a fishing
permit. You can
purchase one online here (
https://www.sportfishingbcs.gob.mx/) - you can
google "Mexico fishing license" and learn more about this.