We've done the one that goes whale watching and the glacier visitor center twice....both times, we had very limited time at the glacier....not enough for us to hike to the waterfall. Last week we were there again and did the smaller tour that does the guided hike. While it didn't go to Nugget Falls, it was a very nice walk that went to the edge of the lake with an amazing view of the glacier (much better than the view from the visitor's center). As an added bonus, we even saw a bear with her two cubs at the end of the hike.
One thing to note that could possibly effect your choice.....the boats on these two tours are very different. The boat they use on the smaller excursion (20 people) is small and on level with the water. The boats they use on the other excursions are larger, two story boats. There are pros and cons to each. After experiencing both, my personal preference is the larger boat, but I can easily see how others might prefer the smaller boat.
I like the larger boat because it has lots of room to move around...you can be in the downstairs part that is heated, or go up on the top deck to be outside. It has two regular bathrooms, and a concession area that sells warm drinks, snacks, etc...and binoculars are also provided for everyone. You also do not feel the motion as much, which is better is you are prone to sea sickness.
The smaller boat....I didn't like it because it didn't have a normal bathroom.....it did have a very tiny "head", but you were not allowed to use it if the boat is in motion. Three hours is a bit outside my comfort zone to not have access to a bathroom, especially when I have my kids with me! The main issue for us though was the sea sickness. I have been on many cruises, and my kids have been on four cruises....and none of us have never experienced sea sickness and have never had to take preventive meds for it....so I wasn't concerned about the smaller boat. Ended up after about the first 30 minutes, my 17 year old son was very sick for the remainder of the time. My daughter and myself started feeling really sick during the last 45 minutes. My husband was perfectly fine, as were most of the other 14 people on board, but I did notice a couple of other people who didn't seem to feel well. So, If you have never been on a smaller boat, you might want to take motion sickness meds as a precaution.
An advantage to the smaller boat is that they seem to get a bit closer to the whales...they can also go much faster. However....on this particular day, we only saw two humpback whales. The other two tours we did on the larger boats....we saw many, many humpback whales, Orcas, and seals....I feel like they went farther and to more places than the small boat did. The smaller boat seemed to stay in a smaller area.
Just my two cents! Honestly you can't go wrong with either choice. Juneau is beautiful!