I picked up 10 5mm Dia x 3mm thick Rare Earth magnets from these guys http://stores.ebay.com/bluestone002
I just installed them on my DIY stirplate and they worked well with my 1" stir bar when placed directly on top of the stir plate. I dont have a flat bottom glass container to test it out with.
I probably have 1/8" (3mm) gap between my magnets and bottom side of my cigar box. The cigar box top is probably 1/8"