Most likely yes. Here are the issues with swap- 3.0 mounts in the front of block not on sides like the v6. If the boat was offered with a 3.0 most likely this mount is already glassed in the boat, if not you have to make one. Second issue is drive ratio-3.0 has a 1.98:1 vs the V6 with a 1.82 :1 so you may be able to go down in prop pitch to compensate but could also not work.
What's wrong with engine in new boat? Cracked block?
Would suggest getting a rebuilt or new v6 longblock and sell your 3.0, you'll have more power and won't deal with any conversion issues. If you can demonstrate a running engine either in the old boat or on a pallet I think you should be able to get $1000 for it, plus other parts like drive and gimbal housing.
New vortec base v6 is $2800 or so, remans are less.