I believe "into" is the better choice, though.
EX: Let's check in
at the desk.
=>
At the desk is where we are checking in.
EX: Lets' check in [/u]to the hotel[/u].
=> *To the hotel is where we are checking in. (ungrammatical)
EX: Let's check
into the hotel.
=>
The hotel is where we are checking into.