So looking for someone who has set off a bomb, stolen a car, killed a security guard, throwing bombs out the car window while shooting at police in pursuit is the incident that you really want to hold up to prove your "liberties" are being violated? There are laws that do allow the police to search your property in certain circumstances depending upon the level of danger to both law enforcement officers and civilians at the time. In Boston the police were looking for a well armed suspect who had already shown no problem with killing. They were not searching private property looking to collect evidence or effect an arrest on the people living on the property the were looking for an armed and dangerous fugitive. If the police had treated the entire situation differently and more people had been killed the public would have crucified the police for not doing anything to prevent it.
On the Federal level the President does have the power to unilaterally go to war on his own but his decision can be overridden if the reason he presents to Congress is later deemed insufficient.
There have been times when the government has clearly violated the law for good reasons. Before the US officially entered WW2 Roosevelt violated several laws that Congress had passed to keep the US out of the war. The vast majority of the citizens at time did not want anything to do with the war in Europe. President Roosevelt felt differently and did what he thought was right instead of what was legal. He used the "Lend/Lease" program to go around the wishes of Congress and supply England with the war supplies they needed. The US Congress had also passed a law banning wire tapping while investigating German and Japanese agents in America at the time. 2 hours after the congressional vote Roosevelt sent the defense department a Presidential order authorizing them to ignore the wire tapping law. These 2 blatant examples of the President breaking the law is more than enough to impeach the President. As it turns out these 2 decisions were vital to the US war effort that the President knew was coming. And even though he broke the law and infringed on peoples liberties he is regarded as one of the best Presidents the country has ever had. Several years ago I watched a round table discussion that included presidents Carter, Bush 1, Clinton, and Bush 2. The question put to them was would they have did the same thing Roosevelt did in the same situation. All of them said they would have made the same choice. Even Carter agreed that sometimes the legal thing is not necessarily the right thing.