There are a lot of companies offering whale watching in Juneau. As in any port, if you book independently you have to check out your supplier.
Frankly I have never heard of either of those, but that doesn't mean anything much. The two most popular independents in Juneau, and the ones that usually get rave reviews on the message boards, are Orca Enterprises and Harv n Marv.
Now to be honest with you, bouncing over the waves in a small boat wearing a life jacket is not really my preferred way of doing things. I would much rather take the ship's excursions which are done by Allen Marine. They have large spacious boats especially designed for wildlife viewing, including "stealth" engines which are particularly quiet so as not to scare the animals.
As Paul says, all the boats are going the same place -- where the whales are. They have spotters out, and word goes on the marine radio to all the boats.
So my personal feeling is that I would rather be sitting comfortably on a bench watching the whales through large glass windows (which the crew cleans constantly) and listening to the on board naturalist. I can see those other boats, with passengers in life vests crowded on the deck. They certainly seem to be enjoying themselves and write rave reviews. It is just not for me. Which is your style?
The best pictures I have of the Allen Marine boats are from Sitka, but the ones in Juneau are substantially similar. Check out our trip report and pictures at Cruising HAL Volendam to Alaska
Whichever trip you choose, bear in mind that those spectacular pictures of whales bubble feeding and breaching are rare. The vast majority of the time you will see a spout, a back rolling above the water, and the flukes as the whale dives. The video on the site above represents our very best whale watching in eight cruises to Alaska.
There are a lot of those two-fer books for Alaska. My personal opinion is that excursions in Alaska are so important and wonderful that I want to choose the very best, not the cheapest.
Have a GREAT cruise!