USS Independence definitely had radioactive wastes aboard, mostly "low-level" and stored in barrels. The ship itself had been contaminated in Operation Crossroads so there wasn't much else they could do with it. There is a survey of the ship from 2015 here: [sanctuaries.noaa.gov
I have a collection of books on disposal of chemical munitions at sea. (I've often thought of writing a book on this topic.) You probably have these sources already. They are at my other residence but when I am next there in a few weeks i'll put together a list to see if there is anything you don't already have.
Finally, I did find in my collection an electronic copy of the TMMC preliminary (7-Dec-45) and updated (4-Dec 47) reports. These are scans of the original paper reports. They do not have the exhaustive list of vessels but there is a lot of discussion of individual ships in them. (The updated report is 102 pages.) Let me know if you need these reports.