Disney-Nautifan
The yellow submarine, which I have seen before in a different photograph, that you are describing is not from Horizons in Epcot. In my opinion, I think it is rather from an old disney film, but I am not entirely sure. However, there is of course the yellow mini-sub that was in the undersea city scene. Both subs are not the same, but the mini-sub now resides in the Backlot Express Restuarant at Walt Disney Studios, Disneyland Paris. Prior it was on display at the Studio Backlot Tour at the same park.
Again answering your question, the boat that you said was also with the Horizons hovercraft and the unknown submarine was in fact from the Special Effects Water Tank of the Studio Backlot Tour at Disney's Hollywood Studios. However, that small boat existed in the show's original incarnation, which existed from 1989 to 2001. After 2001, the water tank was extensively refurbished to its current Pearl Harbour theme. Meanwhile, the small fishing boat dissappeared, and I now presume is with other old props somewhere in the studios, or was destroyed and suffered a more mysterious demise. Other than that, I have unfortunately no idea where this prop now exists. If that is what you saw, then it must have been re-painted in a green colour scheme which you described.
Aside from the fishing boat, a Nautilus submarine from the extinct 20'000 Leagues Under The Sea attraction did actually also sit in the water tank at the studios as part of the landscaping for the show. I saw the ship in 1999 when I visited WDW at the time.
