Hi, with transport we use different prepositions depending on if we can stand and walk or can only sit. For transport where we can stand and walk, we usually use on 'on a train, on a bus, on a ferry, on a boat'. When we have to sit, we use in 'in a car, in a helicopter'. Sometimes we change the preposition depending on the size of the transport 'in a boat' versus 'on a boat' would indicate boats of different sizes. The phrase 'in the same boat' to me indicates a small boat (metaphorically). I disagree with Monica above, and for me the phrase has always been 'we're in the same boat' to mean 'we're in the same situation' - I am only familiar with Australian and British English though.

Small boat. No deck. Get in the boat. (in the hull of the boat) Rowboat, dingy. Big boat, or ship. That is has a deck. Get on the boat. (On the deck of the boat) Yacht, speedboat, anything big enough to have a deck, floors, levels.

in the same boat = trapped inside something / in the same situation this is a figurative speech, not literal.