The thing a bout that is that both cruises will take you to the same place - wherever the whales happen to be that day.
Whales feed in the Juneau area all the time, and there are a few tour companies that specialize in taking people out to see them. They all go to wherever the whales are that day, so you will essentially see the same thing no matter what.
It is a pretty long ride to Auki Bay where the whales feed - about 30 minutes each way, so I would do this....
There are other options as well. If that is the only tour you want to do that day I would try to spend more time on the water, if you see something special you will enjoy it. Optionally, the route to Auki Bay takes you past Mendenhall glacier, so if you can get a whale tour that also offers a stop there it is worth it - especially the bear watch area.
But - if you have plans for Juneau downtown or whatever, then take the shorter whale tour and get back sooner. I recommend you verify how much time they spend ON THE WATER - because as I said travel time is 30-minutes each way, so a "two hour tour" could mean only one hour on the water - don't assume anything.