I will be arriving on Sunday on an international flight from Atlanta (USA) and I plan to catch a Maya Island Airways domestic flight to San Pedro, Ambergris. How much time should I plan for it to take to get off the MD-90 aircraft, collect my checked luggage, clear customs/immigration and get to the gate in time to catch my flight?

Let's start off with what the airport says about taking a flight:
http://www.pgiabelize.com/checkin.htm
"Check-In Counters for all airlines operating out of the PGIA are located in the Main Terminals of the Airport. Passengers are encouraged to arrive at the Airport, 2 to 3 hours before scheduled boarding time to allow for check in and security screening. Airline Counters are located as follows:

Terminal 1
United
Avianca
Maya Island Air
Tropic Air

Terminal 2
American Airlines
Delta

US Airways

Here's the airline service info:
http://www.pgiabelize.com/airlines.htm
It shows the Delta flight arriving around 11:18...but there's no departure shown for any Maya flights...
http://www.mayaislandair.com/san-pedro-a-caye
says there are 11 flights per day from Belize airport
(which explains why the flights aren't shown on the airport website...)

I see that you'll arrive at one terminal and depart from another but it's not a very large facility so your feet won't be tired from walking. The airport website doesn't have a terminal map but I did find this that has lots of photos of the place..including one of Maya's planes:
https://foursquare.com/v/philip-sw-goldson-international-airport-bze-ladyville-belize/4ef22125991151406c289f87/photos
If you have a good phone number to contact Maya I would ask them how much time you should plan on to clear customs, immigration and baggage...they deal with it every day...
so, a lot of information above but no real answers. But oh boy do I (almost) envy you to be going there...have a super super time for all of us not taking a holiday!

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If you sit near the front of the plane, you'll be one of the first passengers off and therefore first in line at Immigration. If you're at the back of the plane, you might have to wait several minutes in the immigration queue -- in my experience, the queue has moved fairly quickly. Immigration itself takes only a couple of minutes.

Then comes the wait for luggage to come off the plane. It could be 5 minutes if your luggage comes in on the first cart, or several minutes if your luggage is on the last cart. If you arrive with only carry-on luggage, there will be no waiting.

Then you carry your luggage through Customs. In my experience, I've never been in a long queue and never had to open any bags so I breezed through in about 1 minute. If you have to open any bags, the process could take a few minutes. If the queue is long, it could take several minutes.

The boarding area for Maya is in the same airport terminal and a very short walk from Customs. If the connection is tight, notify Maya and they will probably hold their flight until you arrive.

The situations where timing is unpredictable are the waits for luggage and any waiting in queues.

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if you don't make one flight they will just put you on the next available.