I have a feeling that some of the unwillingness to make accomidations on the Pirate Cruise comes from the recent death of the peanut-allergic girl who died after kissing her boyfriend who had eaten peanuts hours before. Given that, just substituting something else for peanut butter uncrustables and the normal cleaning the boat gets might not be enough, even if the food is served off of the boat. And, they apparently do allow food on the Fireworks Cruises (or at least are not willing to guarantee that no one brought on any peanut-containing food). So, at least (as others have said), they were honest about their inability to guarantee a safe environment and gave you the information you needed to decide the cruise was not safe for your child.
The same situation would apply to the Albatross Cruise. Even though the kids eat off the boat there, it would be pretty easy to bring peanut residue onto the boat on their hands (or some kids may have eaten peanut buter before getting on, since it is pretty common "kid food"). I'm also pretty sure that boat is used for Illuminations Cruises. So, I'm not sure that they would be able to guarantee a safe environment either, if they really thought it totally through.
I think some of the apparent increase peanut allergies is an increase in people being aware of it.
When I was a school nurse in the mid-late 1980s, there were 2 children I was aware of who had peanut allergies in the elementary school I worked in. Most staff in the school were aware of the one boy, who always had someone who could administer the epipen around because he had needed it once in the past. Most people were not aware of the other other child, who had had much smaller reactions, was older and would not eat anything at school that had been not been brought from home. I'd be surprised if the incidence is that much higher now, but people are much more aware of it because of it being in the news. When the only news you had was the 1/2 national news program and a local 1/2 hour program, a girl who died after kissing her boyfriend who had eaten peanuts would maybe have made the local news, but would not have made the national news. It certainly would not have been broadcast once each hour or half hour, as it was with 24 hour a day news stations.
In the past, if she was in a small town, it would have been one of those sad things that everyone in the town knew about, but probably not outside. To the rest of us, it would be one of those "Is this an urban legend, or did it really happen somewhere" type things.
And, because of the internet, it's much easier to get in contact with other people who have the same situation as you do (whatever the situation is)
There are lots of things we haven't been able to do over the years because they were not accessible for my DD, so I can understand your disappointment. Hope you can find something just as enjoyable for your DS to do.