My wife has been diagnosed with wegeners GPA. She is on prednisone and has been prescribed methotrexate. Are there any less toxic alternatives?

GPA. First of all I wish your wife all the best with full remission of the disease and uneventful maintenance of the remission. The drugs she is on are just fine so long she is followed up regularly by her rheumatologist / primary doctor for adjustment and fine tuning. There are rather more toxic drugs than what she is currently on, good that she is responding to the current drug regimen, best wishes.