The energy stored in this goes by the radius squared. But the centripetal force on the object at the end goes by the radius.
So a smaller faster one is less dangerous, and also requires a less powerful motor (or the motor you have can give you a higher force).
Although the bearings are probably a bit harder to handle when it's faster, the whole thing will weigh less.
On the con side, a smaller one will have a larger difference in force between the top and bottom of the lava lamp, making your experiment less accurate.