There is more to upgrading an alternator than just installing a new larger one.
There will be little advantage to the larger alternator if it is an internally regulated alternator. The internal regulators are typically not set up for charging deeply discharged batteries and are not adjustable for different battery chemistries.
A 3/8 inch single belt is not sufficient to drive the alternator without a lot of belt wear. At 90-100 amp it is necessary to move to a double belt or serpentine belt. The larger alternator will also place more pressure on the adjusting bolt causing it to slip.
The articles on
MarineHowto.com provide a good overview.
MarineHowTo.com - Alterntors & Regulators