It's unlikely that a harbor attack would have involved incendiary or special purpose bombs (although it might have, particularly to destroy fueling and fuel storage facilities). If you assume (and this is guesswork only) that General Purpose explosive bombs were used then the varieties the US Army Air Corps had to choose from were the AN-M30 100 pound bomb, the AN-M57 250 lb. bomb, the AN-M64 500 lb. bomb, the AN-M65 1000 lb. bomb and the AN-M66 2000 lb. bomb. I'm not sure if the B25 ever carried the AN-M66 or not, but I know they were sometimes loaded with 4 1000 lb. bombs (in spite of having a rated payload well under 4000 lbs.). Which bombs were used would have depended partly on availability and mainly on the specific composition of the target. Submarines themselves are very lightly armored, and wooden warehouses on a dock are very easy to penetrate so lighter bombs would have been adequate. Heavier built brick or concrete buildings would have required heavier ordnance. Availability also factors in, the air base would have used whatever they had in stock the day of the mission. Short of finding out the specific unit and locating (if possible) and digging through their paper records of the day of the mission I doubt if you will be able to get any closer than that.

Here is a chart showing every possible type of ordnance used by Army Air Corps bombers in Europe during WW2, you will note the 250 lb. and 500 lb. general purpose (high explosive) are specifically recommended for use against submarines and dock facilities respectively. http://www.303rdbg.com/bombs.html