My wife works from home but the company she works for is in another state. Is that considered making money in another state?

It depends on what state you live in and where the company is located. 

What is your state and your wife's employer state?

How does working remotely affect my state taxes? for additional information.

We live in Florida and the Company is in Boston Mass.

Massachusetts wages will generally be sourced based on where the employee’s work is actually performed, so since you work in Florida, it is considered Florida income.  @electrcian

Thank you