From which site I can download non-coding RNA sequences separately (such as tRNA and rRNA) in a FASTA format?
Obviously NCBI but you might find them hard to find if you don't know exactly what you are looking for. You might try UCSC genome browser (table browser actually) and RFAM.
Rfam is good but how can I get these data separately from Rfam for local blast?
You can find the Rfam family you're interested in and get all the sequences from ftp://ftp.ebi.ac.uk/pub/databases/Rfam/13.0/fasta_files/
Thank you very much Asaf