R: applying function over matrix and keeping matrix dimensions

So I want to apply a function over a matrix in R. This works really intuitively for simple functions:

> (function(x)x*x)(matrix(1:10, nrow=2))
 [,1] [,2] [,3] [,4] [,5]
[1,]    1    9   25   49   81
[2,]    4   16   36   64  100

...but clearly I don't understand all of its workings:

> m = (matrix(1:10, nrow=2))
> (function(x) if (x %% 3 == 0) { return(NA) } else { return(x+1) })(m)
     [,1] [,2] [,3] [,4] [,5]
[1,]    2    4    6    8   10
[2,]    3    5    7    9   11
Warning message:
In if (x == 3) { :
  the condition has length > 1 and only the first element will be used

I read up on this and found out about Vectorize and sapply, which both seemed great and just like what I wanted, except that both of them convert my matrix into a list:

> y = (function(x) if (x %% 3 == 0) { return(NA) } else { return(x+1) })
> sapply(m, y)
 [1]  2  3 NA  5  6 NA  8  9 NA 11
> Vectorize(y)(m)
 [1]  2  3 NA  5  6 NA  8  9 NA 11

...whereas I'd like to keep it in a matrix with its current dimensions. How might I do this? Thanks!