For exammple,
class Lake(Base):
__tablename__ = \'lake\'
id = Column(Integer, primary_key=True)
name = Column(String)
geom = Column(Geometry
http://geoalchemy-2.readthedocs.org/en/0.2.4/spatial_functions.html#geoalchemy2.functions.ST_AsText is what you are looking for. This will return 'POINT (lng, lat)'. ST_X ought to work, though, so you may have another issue if it isn't returning the correct value.
You can parse WKB (well-known binary) points, and even other geometry shapes, using shapely.
from shapely import wkb
for lake in query:
point = wkb.loads(bytes(lake.point.data))
print point.x, point.y