It isn't a question of politeness. In fact, the first is unnatural - we would normally say the second in modern English: 'She is two years older than me'.
The only time it is normal to use 'elder' as an adjective is before the noun, usually to describe sibling relationships, for example, 'She is my elder sister'. 'Elder' has come to be associated with seniority, which is why it is used in this way.
If you are unsure, the easiest option is not to worry about 'elder', and never to use it. You can equally well say 'She is my older sister'. It is never necessary to use the adjective 'elder', as 'older' will always be correct.