In the His Dark Materials trilogy,
Will is totally honest with impressive will power while
Lyra is able to fib her way into and out of just about any situation, though she never uses her talent frivolously! So, given the messages in both their names, LIEra seems the only logical pronunciation; plus there is the beautiful association with the stringed instrument, in English 'lyre', and
Lyra the somewhat harp-shaped constellation.