I've used book 2 of Red Hot Root Words for the past three years with MG-PG 5th graders. It's not the most creative approach (worksheets with matching, fill-in-the-blank, and other standard exercises); besides the worksheets it provides materials for a few good in-class activities that I supplement my own activities with.
For 6th graders I've used Michael Clay Thompson's Word Within the Word and Tamara Green's Greek and Latin Roots of English. The former has way too many errors for me to use it again, which is unfortunate because its approach is very creative and less focused on memorizing words and/or stem meanings than most vocab books I've seen. If your son wants or needs to exercise his imagination using new vocabulary, that's the book to use. Green's book, which is pitched higher than Red Hot or WWW, is organized by subject (human bio and medicine, social sciences, etc.) and uses fairly standard exercises (fill-in-the-blank, etc.).
One good online resource:
www.etymonline.com, which explains the derivations of English words in more detail than, say, merriam-webster.com and is, as far as I can tell, very accurate.
Hope this helps -
