with less than 16 days before I escape the snow & cold, we are planning the details of our trip and have decided to go mangrove kayaking.

The question is what time of day to go: 9am or 3pm? For people that have done it, what is the big difference in the 1 and 2 hour trips? Would the 2 hour be too long for a 6 yr old boy ? (I think the 11 yr old will be OK)

Sue - are you doing the kayak snorkel trip?
I took a 2+ hour kayak snorkel with the the Mangrove Kayak center. You are busy kayaking or snorkeling all of the time - so if you are worried keeping the 6 year's attention - that should not be a problem - but if you are worried about him getting tired - it is work - it depends on how energetic your 6 yr old is.

As for the time of day - I would do it in the morning.

hmmm...
I would not take my six (soon to be 7) year old boy on a 2 hour trip. I can't imagine him being restive enough to watch the birds quietly. It would not be enough physical action for him - paddling does not count that is work. Which means whoever has got him will end up doing all the work and he would complain "there is nothing to do".

Now if snorkeling is involved that is a whole other thing. My kid could spend hours looking at the fish up close and personal.

I'm not sure about a six year old either. I have grandkids 9, 7 and 5 and I did the two hour trip in December (morning one, friend I was with thought it would not be so hot). The naturalist guide was very good/quite knowledgeable it seemed and explained a LOT about the nature and science behind the mangroves, importance of them to the island etc....we found it fascinating but we are both die hard nature fans. I can't imagine most kids under 12 (and then they become young teens and most of them lose their brains <g>) being able to handle that for two hours. Just IMHO for what it is worth.