Nails definitely sink, and can end up trickling down slopes into deeper water. So you might try building a bit of a tower, 2 ladders should suffice, near where you popped the boat then take a few leaps into nearby deeper water and see if they pop into your inventory. I don't generally pop my boats, I just leave them near portals and use a map marker. If I do intend to wreck them then I beach them first.

Other than that, clear the name on your existing portal, dump your stuff in a couple chests, then wander off and get yourself whacked.

When you respawn (hopefully at/near your base) go to the portal you intended to connect and clear the name. Now it should connect with that remote portal so you can retrieve your stuff.

You can rename portals on a return trip as portals will remain linked for a few moments after renaming. I always travel with a blank portal at home. When I get to an interesting spot I slap down an unnamed portal for relaying stuff. If I want to keep the location, I can rename the portal (You need to take care to use a unique name, and Case MaTTeRs) then quickly step through the portal while it is still active to return to home base, then rename that portal to match. It should be deactivated when you arrive and then activate a few seconds after you rename it. Be sure to do it in that order, naming the remote portal FIRST then then home portal. That way *IF* you screw up, you're stranded at home, not timbuktoo.