^^But in 'Tomorrow is Yesterday', they were low enough to be seen by Captain Christopher in his fighter jet. If they were that low, then they WERE in the atmosphere. There's no way they could have been seen otherwise.
Did they ever say how high there were in 'TiY'?
Not directly... but it would be easy to figure it out.
All you've gotta do is figure out what the aircraft Capt. Christopher was flying (I'm thinking it was an F-101, but I might be mistaken), find out the maximum operational ceiling for that aircraft (since it's no longer an aircraft we fly, that info should no longer be classified)... in the episode, Capt. Christopher is near his maximum ceiling when it spots Enterprise (thats why, I always assumed, he was unable to climb to the same altitude as Enterprise before it started it's own ascent) He was about a half-mile below the Enterprise, and about the same distance behind it. So add that amount to the max operational ceiling for that airplane and voila... you know where the Enterprise was.