set.seed(1234)
M = matrix(sample(20,20), ncol=4)
M
     [,1] [,2] [,3] [,4]
[1,]    3   10    7    9
[2,]   12    1    5   17
[3,]   11    4   20   16
[4,]   18    8   15   19
[5,]   14    6    2   13
t(apply(M, 1, function(x) head(order(x),3)))
     [,1] [,2] [,3]
[1,]    1    3    4
[2,]    2    3    1
[3,]    2    1    4
[4,]    2    3    1
[5,]    3    2    4