Which is better academically (preferably CSE and ECE branch), NIT-Manipur, NIT-Meghalaya, NIT-Sikkim, NIT-Nagaland, or Tezpur University?

If your need is a job right after graduation, then NITs certainly are good alternatives. In this scenario, NIT Meghalaya & Nagaland would be safer. But don't expect dream companies on-campus placements. The university of Tezpur can also offer you few IT placements, but TU placements are not comparable to the NITs.

TU will be the best choice amongst those listed if you want to learn, explore, study ECE, CSE fields. The University of Tezpur has great ECE & CSE departments. Both departments are over ten years old. In comparison with NIT-Silchar, TU's CSE faculty & labs better. TU has a strong research orientation, since many science and engineering departments exist, which is not the case for all the NITs listed. 

So, if you want placement, go for the NITs. If you want to learn and explore your field then TU is definitely the better choice.