When I try to get sql performance counters from a server that has more than 1 instance of SQL I keep getting this error:

Cannot find any performance counter sets on the localhost computer that match the following: \MSSQL$DEV:Databases

Here is the code:

Get-Counter -ListSet SQLServer:Databases | Get-Counter

How can I change it to get the specific instance counter?

Install the counters for the second instance.

Post this question in the SQLServer forum.  They will help you fix the missing counter sets.

https://support.microsoft.com/kb/227662

Start here and post any further questions on this issue in SQS forum.