I am currently trying to get the NDK up and running in Eclipse. I have read several tutorials, and found one that seems to make sense to me. However, it says:
I was able to generate an NDK development environment in Eclipse by using the information on the ARM site (http://ds.arm.com/ds-5-community-edition/).
There are some caveats to using the NDK. For instance, if you installed it in a path that has spaces embedded (for example C:\program files (x86)\Android) you'll run into problems.
Try to run the ndk-build.cmd command in a command prompt to see if you have any problems with your installation.