According to MLB.com, the Cubs have three of the top 50 prospects in all of baseball.
Javier Baez, a 20-year-old shortstop, came in at number 16, Abert Almora, an 18-year-old center fielder, is number 39, and Jorge Soler, a 20-year-old Cuban outfielder, is at number 42.
The full list is here.
The Twins and Cardinals each have four of the top 50, and the Rays & Mets have three. The White Sox have zero. (Their highest ranked prospect comes in at #68)