Metaballs

If you need to use metaballs, they recently (October 2015) got approx 10 fold speed increase!

See this blender.stackexchange.com question that spawned this example. There's also more information given by various authors. The snippet below covers the basics that might otherwise not be obvious.

import bpy

scene = bpy.context.scene

# add metaball object
mball = bpy.data.metaballs.new("MyBall")
obj = bpy.data.objects.new("MyBallObject", mball)
scene.objects.link(obj)

# test with different values, for viewport do you need ultra high res?
mball.resolution = 0.16  # View resolution
# mball.render_resolution = you decide

# first metaball element doesn't exist yet - create it.
ele = mball.elements.new()
ele.co = (0.0, 0.0, 0.0)
ele.use_negative = False
ele.radius = 2.0

# adding extra metaball elements to the object 
ele = mball.elements.new()
ele.co = (-0.726, 1.006, 0.559)
ele.use_negative = True
ele.radius = 0.82279