As mentioned above sure you can purify using the Ni-NTA resin. You should not encounter any reduced yield, but you can perform a second step of purification by affinity if after the Ni column your protein is not clean enough. Then you should cleave the MBP tag as it is 370aa more that you don't need.
Thankyou for adding answers..I was facing a chaperone after the first step of purification through amylose resin..was finding ways to get rid off that..it's the one I was getting around 63 kD...