I bought .25"x.25" square rare earth magnets and they seem to work fine. The 3/8" discs should be great. You just want to make sure you get the polarity right before you secure them. Make sure one is North and the other is South.
The bar magnets are great if they are magnetized through the length. The one you listed appears to be magnetized through the thickness. That means that one 1"x1/4" surface is North and the opposite is South. This is bad for a stir plate. You would want a bar that is magnetized through the length so one end is North and the other is South. If you don't, then you will probably throw your stir bar.
A great alternative is the magnet from an old or broken computer hard drive. You will need a Torx bit screwdriver, but those magnets are strong and magnetized along the proper axis.