It sounds like you have a heavy boat - what is the Type/Brand? Length? and weight of the hull? If your previous engine was a 2-cylinder engine and you're trying to compare it to a single cylinder that may be where you problem lies. 2-cylinder and 1-cylinder engines will act very differently when trying to push heavy loads.
I have a Beneteau F235... Factory says it is 2300 lbs but most owners that have weighed them would say 3300 lbs or better.
yes 1 cylinder is different than 2 cylinder and two stroke vs 4 stroke is different. I would expect a 6 hp 2 stroke to run stronger than a 6hp 4 stroke by some small margin. but not a 6 hp 4 stroke to run weaker than a 4 hp 2 stroke.