You definitely could say it that way. Personally, I think that "It has been a long time since I've seen you" sounds a little more natural. ("I've" is a contraction of "I have" - and sounds more natural).

As Eve notes, you could use the perfect tense here, and generally would in the usual context where you are face to face at the time and expect to see each other on a continuing basis. But simple past is fine, too, especially if you are talking about an opportunity for seeing each other that is no longer current, for example, if your friend had moved away and you are talking on the phone.