We received a 1099r for a check that we did not receive. A new check has been issued, but we have not received it yet. Do we claim it for 2016 anyway?

Yes. This would still qualify as income in 2016 based on how the IRS interprets it. Alternatively, you can wait to make sure the check arrives for the exact amount stated in the 1099-R, but that may require you to amend your 2016 returns.