Here's what ended up working. It's kind of convoluted, and I'll admit that I don't quite understand why it works, but it does work.
SELECT Site, Warehouse, ROW_NUMBER() OVER (PARTITION BY Warehouse
ORDER BY Warehouse) AS RowNum
FROM(
SELECT Site, Warehouse, ROW_NUMBER() OVER (PARTITION BY Warehouse
ORDER BY Warehouse) AS RowNum
FROM Table1) AS T
WHERE T.RowNum = 1
The solution was adapted from the answer to this question: "Invalid column name" error on SQL statement from OpenQuery results