You can do with either APM or UIM using PerfMon.
In the case of APM, It depends on the counters you want. Some are instance-based, like the queues.

So if I generally want all of the counters for queues, I'd do something like this:
|MSMQ Queue|*|*,|MSMQ Service|*
Remember to start each filter with a pipe "|" symbol.