In diplomacy screen you can request that an enemy "withdraw his forces." What the manual (and the strategy guide for that matter) doesnt tell you is that this refers to *all* enemy forces, including stealth units. If you request an AI to withdraw and they say "yes" then they will remove all their units, including stealth units (most of the time anyway
)
If this doesnt work you can try:
1) Build "The Agency"
2) Put spys on all major roads/choke-points of your civ
...and if all else fails....
Build a stack of 12 tanks and roll over the spying bastards; this is how my all my "diplomacy" works - try it.
Hope this helps!