Kona, Sorry no one has responded to your post yet but I'm sure there will be someone who has recently been on the Victory respond. I personally have sailed the Victory and have sailed from San Juan many times, although it's been a few years since I was there. But to be specific about a certain check in time is a little hard to do.
First of all, the ship has to be cleared by Customs and Immigration, which can, at times due to a variety of reasons, take longer than others and there's not a set rule-- when the ship docks, the officials are in charge and the Cruise Line simply has to abide by the officials whims.
Normally you should be aboard by 11:30 or 12 but don't take that as gospel-- sometimes a little earlier, maybe sometimes a little later. The cabins are normally ready by around 1 p.m. If you get aboard by around 11-11:30 or so, just head for the buffet and have a leisurely lunch and explore a bit and by then the cabins should be ready.
I would think the above would be a general guideline but hopefully someone who has recently sailed from S.J. will be of more help.
What time does your flight get into S. J.?