IANAL, and don’t work for Numenta, but have discussed this with people there. This is my understanding.
If you’re not using NuPIC, then this depends on a) what license you use for your implementation (AGPL only applies to NuPIC itself), and b) what potentially Numenta-owned IP you incorporate in your implementation.
This is a grey area, because Numenta has only explicitly placed their patents and IP into NuPIC (and possibly now HTM.java), not into anything developed independently. Their informal attitude (ie this is not their legal declaration) is that a project which uses the AGPL or equivalently strong license, and refers to Numenta for commercial licensing, will not have a problem.
One thing is for sure. If you use any Numenta-owned IP for your project and do not open source it, then you’ll have to talk to Numenta about what that implies.