Taking a quick look. There's probably more you can do.
1. Eliminating the anonymous function call on the conditional inside the inner loop should save you some time since it has a healthy amount of overhead (unless Mathworks did some magic in 2016b's JIT). I'd see what inlining it right under the ~(w < ts) does for speed.
2. You're going against MATLAB's memory indexing, which is column major order. Since your inner loop i is striding columns you're paging RAM like nobody's business. Can you rearrange the data so that the inner loop is the one looping on the rows? You want to go down rows on your inner loop. I think you can just do a transpose on how you're storing your data in this case.
3. If you're only altering the seed every 1000 rows, why not grab your rand() call then rather than call it inside the inner loop 100k times? If you've got the RAM to spare. rand is fairly quick, so I'm not positive this will outweigh the memory hit. Depends on the size of the vector, I'd wager.
4. It doesn't seem that your j's are interacting with previous ones (which makes sense since you're doing this stochastically). So, MATLAB should no problem treating this as a parfor loop. The outer loop should be the parfor one.