Your idea for x & y sounds fine. Your example is 3x3 which I find a bit confusing. I might expect points along a line to look like:
array = { {0,0}, {1,1}, {2,2}, {3,3} )
where each pair is {x,y}. Then again, in some problems I might define a game board as {row,column} or {rank,file} which are really {y,x}. It kinda depends on the problem domain. Make your method parameters and variable names as clear as possible to help out the reader.
Oh, and think about using the Point class you get free with
Java. Then you have a one-dimensional array of a useful and standard object!