I've done Boston harbor cruises in the past --- more than 5 years ago --- and I remember just bringing my own sandwich, chips, dessert, etc. b/c I didn't want to deal with it. That's my fallback, as an adult w/ PA/TNA/shrimp to just bring my own food, sometimes I just don't want the hassle and concern when doing something fun, to worry about the food or any possible reaction.
That being said - what you should do is call them and talk. You'll be able to to gauge if they "get it" and if their procedures fall within your comfort zone. If it doesn't, so be it. You have your back-up plan
If it does, then yay! Sometimes what they (caterers/food service) do is to make separate plates for the allergy folks and put them aside and label. Then during the event/dinner service you have to find the head waiter to get the special plates. I've done this at conference dinners and such successfully.
If, what they do doesn't fall within your comfort zone --- you can let them know. Saying gracefully, "We are new to the allergy, and you know, really insecure. We'd all like to have fun and not worry about the food. I would like a letter emailed to me that we have permission to bring with us food for my DS --- homemade sandwich, salad, etc. --- that we'll keep in a cooler bag. We'll just need maybe a plate for him so he can eat with us at the table? Thank you so much for accommodating us!" Said nicely, and without demand, it can get you the exception to bring on food no problem. Or --- you can just do it! Just do it, bring on a soft-sided cooler pack in a backpack...don't ask for permission. And if you get stopped or questioned - just say the allergies are super severe and you cannot risk him eating the catered food. That usually works. Just gotta be nice about it. Play ignorant to bringing it on board. If it's not going your way - use the 'hidden disability' card.
There are lots of options presented above, various strategies I've used over the years.
Good luck!
Adrienne