Short answer
Primordial black holes and associated worm holes may be a key to harnessing, and overcoming the limitations of gravity.
Background
The general relativity theory of Einstein basically says that gravitation is not a force, but instead a manifestation of the curvature of space-time (source: NED). Basically it states that a massive object does not pull on another object, but that instead it bends space-time such that it appears to be pulled to the massive object by a distant observer (Fig. 1, upper panel).
Now, you don't want your super heroes to be like Atlas tossing around heavenly objects. Here, black holes become interesting, because they can be as massive as stars and beyond, but can be substantially smaller, because their density is infinitely larger than a celestial body. Black holes are regions in space where the pulling force of gravity is so strong that light is not able to escape. The strong gravity occurs because matter has been pressed into a tiny space. This compression can take place at the end of a star's life and some black holes are a result of dying stars. Because no light can escape, black holes are invisible without sophisticated observation equipment (source: New Scienist, 2013).
Black holes can come in a range of sizes, but there are three main types of black holes, dependent on its mass and size. The larger two types, i.e., the stellar (and most common) and supermassive black holes are not of too much use for your story line I guess. However, the smallest type is known as the primordial black hole and this type of black hole can be as small as a single atom, albeit with the mass of a large mountain (source: New Scienist, 2013).
Now, such primordial black holes may be the gateway to singularities. Singularities are the core of a black hole, where the gravitational field is infinitely strong. At that point, entering it will likely cause anything to be crushed to an infinite density. However, general relativity provides no basis for what happens next. Basically, at thus point, all our known physics law cease to apply and all known equations break down (source: New Scienist, 2013). Different models explain the behavior of travel within a singularity differently. One model predicts that eventually gravity again reduces and objects can re-appear in another part of the universe, or another universe altogether. This has been described as a worm hole (Fig. 2). Worm holes are your gateway to, well anything related to gravitational tricks I guess (pun intended).
Fig. 1. Black hole (top) and singularity (bottom). (Top) Einstein’s general theory of relativity states that gravity is a curvature of space-time. A massive object, such as a star, deforms space-time, such that another object such as a planet or a light beam follows the shortest path (a “geodesic”) on the space-time grid. To an observer, this looks like a deflection of the trajectory of the planet or light beam caused by gravity. (Bottom) A black hole can be so dense and massive that it creates a region of infinite curvature (a “singularity”) so that inside the event horizon light cannot escape. source: NED)
Fig. 2. Visualization of a worm hole. source: Physics of the Universe