The problem of the missing apkbuilder.bat is not coming from the Android NDK but from the Android SDK. Google, in build tools r22 moved some files in different directory, breaking rhodes and a lot of other Android tools.
You've different options:
- Use RhoMobile Suite v4.0
- Stick to RhoMobile Suite v.2.2 downloading the latest v3.5 rhodes gem from github (using the 3-5-stable branch).
- Use Android SDK build tools r21
more information are available on Launchpad, the RhoMobile community site by Motorola Solutions.