I was in Juneau a couple of years ago on July 4th. The parade is fun and the fireworks on July 3/4 were nice. We did have quite a bit of rain over the course of the several days we were there, but it didn't stop us from doing much. Just plan on it.
Note that the public bus system won't be operating that day and traffic downtown will be snarled in the morning and into the early afternoon with the parade.
You might consider taking a whale watch trip with one of the operators. I have used Harv & Marvs in the past and have been more than pleased.