Ndoye, a 7-foot-0 senior, had 11 points, six rebounds and five blocks at halftime as St. Bonaventure held a 35-25 advantage.
Andell Cumberbatch had 16 points for St. Bonaventure (4-1) and Dion Wright added 14.
Karonn Davis and Ramone Snowden scored 13 apiece for Niagara (1-3). Rayvon Harris added 10. The Purple Eagles made just 19 of 52 field goals (36.5 percent), hit 14 of 22 free throws (63.6 percent) and turned the ball over 20 times.
Harris' basket brought Niagara within 26-23 with 3:13 left in the first half, but St. Bonaventure went on a 9-2 run to close the half with a 10-point lead.
St. Bonaventure went on a 9-0 run late in the second half for a 23-point lead.