There is no such tool that reliably identifies all non-protein coding RNA's de-novo, you need to use a chain of tools and then from my (limited) experience the predictions are pretty bad compared to protein-coding gene prediction for some. The most popular tools:

• RNAmmer for ribosomal RNA
• trnascanSE for tRNA, which has pretty high accuracy

For the rest of ncRNA you need some experimental evidence from sequencing.

Try lncRNA-screen