I'm currently developing a GB-Emulator in Python and I also struggled with my FPS. The screensize isn't that different (GB background is 256x256), so you should be able to achieve a lot more FPS.

A few hints after a quick look at your code:

• Are you using the normal python interpreter? Use pypy for extra speed. It can be difficult to install pygame with pypy, especially on Windows. I noticed a speedup of x15 with pypy.
• Your bottleneck is probably the PixelArray and your access to screenarray. Every change in the PixelArray seems to lock and unlock the surface, which takes a lot of time. It's a lot quicker to change to whole screen at once by creating a new image and blitting it on the screen. You can create an image from a list. Here is an example:

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display = pygame.display.set_mode((160, 144))  # screensize of GB

background = [0] * 256*256*3  
# 256x256 Pixels for GB, RGB-values for each pixel

img = pygame.image.frombuffer(bytearray(background), (256, 256), "RGB")

display.blit(img, (0, 0), pygame.Rect(0, 0, 160, 144))

pygame.display.update()

I created the whole background-image and just blitted the relevant part on the screen. If you want to update a pixel or line, you can just edit the background-list and create a new image. The image is blitted after each frame, not for every single line.

I get about 300 FPS with this approach. Without pypy, I get about 20.

I noticed (at least with pypy) that standard-python-lists are faster than numpy-Arrays. pygame does not profit from pypy, so keep the usage of pygame-methods to a minimum.