There's a lot of confusion amongst GPs over the use of thrush meds, mostly because many of them aren't licensed for lactation (although they're so widely used that they're shown to be safe).
Nystatin drops are often given to the baby, but it's in a sugar solution which can feed the thrush and make it worse (thrush thrives on sugar).
Daktarin GEL is for the baby's mouth and is not suitable for nipples as the carrier gel doesn't sink into the skin properly. Daktarin cream is the same drug (miconazole) but in a cream based carrier which will sink into the skin. Daktarin gel is sometimes not given to young babies (under 4 months) because it's really thick and is considered to be a choking hazard. However, a tiny smear on the finger rubbed over the gums and tongue is fine if done carefully (a new smear for each mouth section).
Clotromizole (Canestan) is sometimes given to mum but it can trigger skin reactions. Daktarin (miconazole) is less likely to.
Fluconazole is used to treat vaginal thrush in low-ish dose, one-off treatment. It can be used to treat thrush within the milk ducts but a higher and longer-term dose is needed. It's not required if the thrush is on the skin only, but is generally needed when it's in the milk ducts. It's not licensed for lactating women because there are no safety studies done by the licensee (you can't do studies on lactating women!). However, the amount of the drug that passes to milk has been studied and is less than is licensed for babies - so is considered to be safe to use while breastfeeding. But if the GP or pharmacist just looks at the drugs list they won't see this.
This is a really useful leaflet: www.breastfeedingnetwork.org.uk/pdfs/BfN_Thrush_leaflet_Feb_2009.pdf
Finally, watch out for hygiene as thrush is highly contageous. Be really, really careful about hand washing after nappy changes and wash anything that touches the affected skin on a 60 degree wash or hotter. Looking into grapefruit seed extract as a complimentary treatment is worthwhile.