Converting rectangles into polygons

There are several possible approaches, but they all depend on what is in your source file.

So, clarify it and, if possible, provide a sample Illustrator file for inspection.

Also, what kind of polygons are you going to create?

Astute Graphics' Phantasm plugin for Illustrator can convert a pixel-based image into a vector halftone pattern. Unfortunately the plugin doesn't have any settings to allow a one for one conversion where you're getting a colored vector shape for each individual pixel. The only filter or effect I've seen that can do this is the Pointillizer filter in CorelDRAW. I'll use that for creating accurate simulations of LED-based "jumbotron" displays in sign design sketches.

IF you use vectors to create pixel art, you may use a script like zamena-size to replace the rectangles by a Polygon with 4 sides.

Szymon,

"I have a pixel art piece made of rectangles,"

If this is a raster image, it only consists of pixels (coloured squares) with no way to change the individual apparent paths.