Here's an interesting test of various antibiotics: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3132871/

It looks like different agents are more or less effective for different forms of the disease. This study didn't look at Ceftriaxone as far as I can tell, which is what is usually used for later stage Lyme disease. Doxycycline is typically used for prevention, which makes sense because you're probably less likely to have cysts forming immediately after infection. It doesn't look like Metronidazole is as effective against non-cyst form Lyme disease.

Doxycycline treatment reduced spirochetes by ∼94%

Metronidazole treatment reduced spirochetes by ∼54%

and

Tinidazole treatment reduced round bodies by ∼94%

Metronidazole treatment reduced round bodies by ∼68%

Looks like Tinidazole might be even better than Metronidazole vs. cyst-form Lyme disease.