crypto now supports base64 (reference):
cipher.final('base64')
So you could simply do:
var cipher = crypto.createCipheriv('des-ede3-cbc', encryption_key, iv);
var ciph = cipher.update(plaintext, 'utf8', 'base64');
ciph += cipher.final('base64');
var decipher = crypto.createDecipheriv('des-ede3-cbc', encryption_key, iv);
var txt = decipher.update(ciph, 'base64', 'utf8');
txt += decipher.final('utf8');