Second seed Cheruku came back from a set down to beat Nikshep 2-6 6-2 7-5 in an engrossing two hours and 25 minutes battle for the title.
In the girl's under-16 category, second seed Gujarat girl Zeel defeated Ramya Natrajan 7-5, 6-0 in one hour and 25 minutes.
The under-14 boys' title was claimed by Chandigarh boy Digvijay P Singh, who upset top seed Siddhant Banthia 6-3 6-0, while the girls' title in the under-14 category was won by Sathwika Sama who defeated Sabhyata Nihalani 6-2 6-2.
Nikshep later revealed that he had injured his right elbow during the semi-finals.
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"I was playing with pain killers and finding it difficult while serving, but credit to him the way he fought back," he said.
Results:
Boys Under 16 Singles
Vashisht Vinod Cheruku (2) (KA) bt BR Nikshep (1) (AP) 2-6 6-2 7-5.
Girls Under 16 Singles
Zeel Desai (2) (GJ) bt Ramya Natrajan (TN) 7-5 6-0
Boys Under 14 Singles
Digvijay Pratap Singh (CH) bt Siddhant Banthia (1) (MH) 6-3 6-0
Sathwika Sama (AP) bt Sabhyata Nihalani (DL) 6-2 6-2.