I gather BIP39 is a seed/mnemonics generating algo and has nothing to do with BIP49(BIP44), these are two different algo.
Essentially yes.
BIP stands for Bitcoin Improvement Proposals. Each one is a separate proposal for some new feature to be added to bitcoin, although many BIPs build on the work of previous BIPs. You can read about all the BIPs here:
https://github.com/bitcoin/bipsBIP39 is entitled "Mnemonic code for generating deterministic keys", and as you say, lays out how to generate a mnemonic phrase from a seed and vice versa.
BIP44 is entitled "Multi-Account Hierarchy for Deterministic Wallets" and lays out how to derive multiple addresses for multiple coins and accounts from a single seed.
BIP49 is entitled "Derivation scheme for P2WPKH-nested-in-P2SH based accounts" and lays out a similar thing to BIP44 for nested segwit addresses.
As you say, BIP39 is focusing on a different issue than BIP44 and BIP49.
To back to your original question - yes. You can use the same mnemonic phrase in both Electrum and MEW to recover your bitcoin and ethereum, respectively. Just be aware that once you have entered your phrase in to an electronic device, it should be considered compromised (in case your device has malware, your connection is being monitored, or something similar you are unaware of). I would recommend recovering all your coins as quickly as possible and transferring them out to new, secured addresses.