Which is better: leaving the salary in a Riba-based bank so it benefits from the balance, or transferring it to an Islamic bank while a portion of the salary is deducted by the Riba-based bank?

If you can transfer your salary from an interest-based bank, then do so, because leaving money in it is considered a benefit to the bank for its use in usury. There is no contradiction between this forbidden benefit and what the Islamic bank deducts for the transfer, as this is a permissible fee. Leaving money in an interest-based bank when one is able to withdraw it is considered assisting the bank.