Both of them have the same meaning. BUT I would use いまどこですか to emphasize "NOW" In general, you can use both of them.

I would use いまどこですか？because you clearly asked them where they are 'now'. If you were just saying 'Where are you?' you could have used どこにいますか？ but since you specifically said 'now' you would use the first one. Like the previous user said, in general both can be used. But in your case it's the first. Hope that helped ^^

like cory said this should be in the japanese section, but usually i'd go with いまどこですか since どこにいますか is probably less used and grammercally incorrect... ima doko desuka is literally right now, where ?. where as doko ima desuka is where, right now. usually people would also throw in an indentity in front like anata wa or kimi, ima doko desuka for the you bit. but just いまどこですか is fine being colloquial and informal

You need to switch your languages on the question. You specified learning English for Japanese speakers instead of the other way around.