there are loads of ways to achieve this..

How many rows of data are we talking about in the tables? if we're talking a few thousand and you are able to add a linked server then just join on the id's and add a where clause that compares the second column.

If you're not able to add a linked server, then bcp/ssis/use openrowset to copy one set of data to a temp table on the other server to do the compare.

If you have millions/billions of rows to compare then, you will need to do a few more steps, like ssis across the records, maybe in batches and you'd probably want to index the joining column, but then the tecnique is the same.

hope this helps.