The ride on a boat to the hotel from the train station is relatively short - depending on your hotel's location. Also, there isn't much "ocean motion" in the Venice canals, so motion sickness - while possible - is not likely. If you don't get motion sickness riding a city bus while you're standing up, it seems unlikely (to me) that you'd get motion sickness on the boats in the canal.
I suggest, though, that if you're the least bit queasy, you try to stand in the very front of the boat and look out - rather than at friends with you... Eyes on the horizon helps soften motion sickness... Alternatively, stand at the back of the boat and admire the city rather than chat with friends.
I can't speak to the length of the walk from the train station to San Marco with luggag, but Venice is very walkable.
Maybe try the boat and if it's really too much, hop off at the next stop and walk the rest of the way.