Oh, you have the perfect combination of plants to cause cedar-apple rust disease (Gymnosporangium juniperivirginianae). Yes, as an organic gardener I try to find the best possible non-toxic way to control plant diseases. Here's what I found:

Symptoms

Cedar apple rust is a fungal disease that requires juniper plants to complete its complicated two year life-cycle. Spores overwinter as a reddish-brown gall on young twigs of various juniper species. In early spring, during wet weather, these galls swell and bright orange masses of spores are blown by the wind where they infect susceptible apple and crabapple trees. The spores that develop on these trees will only infect junipers the following year. From year to year, the disease must pass from junipers to apples to junipers again; it cannot spread between apple trees.

On apple and crabapple trees, look for pale yellow pinhead sized spots on the upper surface of the leaves shortly after bloom. These gradually enlarge to bright orange-yellow spots, which make the disease easy to identify. Orange spots may develop on the fruit as well. Heavily infected leaves may drop prematurely.

Treatment

• Choose resistant cultivars when available. (See list of resistant cultivars from Clemson University.)
• Rake up and dispose of fallen leaves and other debris from under trees.
• Remove galls from infected junipers. In some cases, juniper plants should be removed entirely.
• If this fungal problem continues, organic disease-fighting fungicides can be applied weekly starting with bud break on apples and crabapples.
• Contact your county's Cooperative Extension Service for other possible solutions in your area and more information on proven resistant cultivars.

Note: Fungicide applications are used to protect the tree from spores being released by the juniper host in mid-spring. This occurs only once a year, so additional applications after this springtime spread are not necessary.

Courtesy of the NYBG Plant Information Service