In fact you don't need to extract the geometries your self - just create a filter and iterate through the filtered collection. In your case there will probably be only one feature returned.
Filter pointInPolygon = CQL.toFilter("CONTAINS(the_geom, POINT(1 2))");
SimpleFeatureCollection features = source.getFeatures(filter);
SimpleFeatureIterator iterator = features.features();
try {
while (iterator.hasNext()) {
SimpleFeature feature = iterator.next();
Geometry geom = (Geometry) feature.getDefaultGeometry();
/*... do something here */
}
} finally {
iterator.close(); // IMPORTANT
}
For a full discussion of querying datastores see the Query Lab.