Let me address the influence of special interest groups on the Judicial Branch of government first, as it is quite elementary.
Ideally, there is little to no outside influence on judicial processes. Day-to-day functioning of government involves Executive-Legislative interaction. Once judges (in the federal system, anyway) are nominated by the president and confirmed by the Senate, any further political interference with the workings of the judicial system is largely avoided. That is not to say that special interest groups do not attempt to influence the judiciary, as they clearly do on core issues like capital punishment, abortion, and gun control, but in order for the judicial process to function, it needs to be insulated to the extent possible from political interference.
The influence of special interests on the Legislative Branch of government, on the other hand, is substantial, both by design and in practice. Congress -- and I spent 20 years working as a congressional staffer in both the House of Representatives and the Senate -- was intended by the authors of the United States Constitution to be that branch of government most directly answerable to the public. Certainly, levels of influence on the part of special interest groups can prove excessive, but limiting that influence is politically, legally, and morally difficult. Any individual or group that seeks to influence the legislature is by definition a special interest. That are some are large and well-resourced while others are small and lacking in resources should make no difference, although, in practice, it often does. The point, however, is that lobbying is an inherent and, much of the time, positive element of government.