I have two search boxes on the page. First one is the universal search in the main navigation bar and the other one to filter map pins based on location. What do you guys think?
Its fine till your user understands if they are distinct or similar. You might want to change the placeholder "Search" to "Search Location" or "Search by location/country/city" whichever clarifies its use.
As Avish Vijay stated, in my personal opinion it's not necessarily a bad idea to have two searches if one search is a global search and the other is contextual to the function on a certain page. It's important though to underline the difference with the contextual search though and currently you're not clearly conveying why the contextual search is different from the global search.
By the way, why is the magnifying glass icon and the global search link in the top nav bar on a separate row? I don't quite understand the screenshot as it is.