Hi Chris,
Thanks so much for stopping by the Disney Parks Moms Panel! When I saw your question, I could not wait to dive in to answer it!
I distinctly remember my first visit to Walt Disney World when I was little and riding 20,000 Leagues Under the Sea stood out as a highlight of the day. It's hard to believe that more than 20 years have passed since Captain Nemo's Nautilus submarines took their final voyage. Once the ride closed down, the 12 submarines were removed. Legend has it that two were submerged off Castaway Cay for snorkelers to enjoy, but have since been removed, and one was used for a time as part of the now-closed Studio Backlot Tour. Unfortunately, I'm not aware of any locations on property where one of the Nautlius submarines might be seen today.
I have heard there are a couple hidden Nautilus references in Fantasyland today, right where the ride was once located, though I haven't had a chance to check them out myself. The first is inside the tree as you enter the queue for The Many Adventures of Winnie the Pooh and the second is a carving in the queue to Under the Sea ~ Journey of The Little Mermaid.
Another fun stop I'd suggest for your son is
Trader Sam's Grog Grotto at Disney's Polynesian Village Resort. You can see some artifacts there that cleverly hint to 20,000 Leagues Under the Sea...and there's even a special drink on the menu in its honor called "Nautilus" that includes a submarine-shaped mug that would make a spectacular souvenir. I'm not sure of the age of your son, but kids are allowed in Trader Sam's until 8:00 p.m. Just be sure to arrive early (before opening at 4:00 p.m., if possible) to avoid a long wait for this super-popular spot.
I hope your submarine scavenger hunt goes swimmingly, Chris, and wishing you a magical vacation!
Beth