Yes, Both courses are Masters course in Engineering (Except BS-MS which relates to Basic Science ). Also, MTech/ME admissions usually depend only on GATE scores, MS admissions usually consist of entrance examination score plus interviews. MS is more of research oriented whereas M.Tech is more of technical and course oriented. Duration of M.Tech is 2 years and MS is of 1.5 to 3 years.

Note : Both are course wise different so I would suggest you to choose the one in which you have maximum interest and in which you can give your best.

Good Luck!!!