By murdered do you mean died of violence? I'm not sure you can include those that died in raids or battles as being murdered, unless they were unarmed.

If by "murdered" you mean killed in battle or violently, far fewer than died from European diseases.

Let's look at the original "Conquistadoring" period, when the Spanish conquered large and densely populated Native American societies.

Cortez had about 600 men when he landed in Mexico. He fought a series of skirmishes and battles against the Tlaxcalans before they made an alliance against the Aztecs. Total number of people killed in these battles is unknown but probably small.

Then Cortez marched to the city of Cholula. The Spaniards became convinced that the Cholulans were planning to attack them in the night. They burned the city in the "Massacre of Cholula". Cortez claimed that 3000 Cholulans were killed (though many would have been killed by the Tlaxcalan allies).

Then Cortez marched to Tenochtitlan where he took Montezuma captive. His next battle was taking part of his force (300 men?) out to defeat a Spanish Army of 900 which had been sent to arrest him. He beat them in a night attack, took their commander prisoner, and persuaded the surviving Spanish force to join him. Casualties probably few.

When Cortez got back to Tenochtitlan, he found that his men there had massacred a bunch of Aztec nobility at a religious festival (the Spanish claimed they were trying to stop the human sacrifices. The Aztecs claimed the Spanish wanted the gold the nobles were wearing). There were said to be 600 Aztec nobles in the Main Temple. Most were killed.

Then Montezuma died (killed by Cortez?). The Spanish had to flee the city. They were cut off at the Battle of the Causeway, and had to fight their way out. Some 600 Spanish (almost half) were killed or captured. More than 1000 Aztec warriors were killed.

As Cortez tried to flee to the safety of his allies the Tlaxcalans, they were cut off by the Aztec Army, and had to fight the desperate Battle of Otumba to survive. The Spanish infantry held their line against wave after wave of assault, while the Spanish cavalry charged again and again through the Aztec ranks. The cavalry finally managed to kill one of the Aztec leaders, and the Aztecs withdrew. Just in time for the exhausted Spanish. They had many casualties. Almost all the survivors were wounded. They had only 20 horses left alive. Aztec casualties were probably several thousand.

Then Cortez joined the Tlaxcalan, and they launched a campaign to take all the Aztec dominated cities one by one, most by diplomacy, some by battle. Most of the killing was by Spanish allies, but they probably killed another thousand or so.

There was then an eight month siege of the city of Tenochtitlan. During this siege, smallpox hit the Aztecs and the allies, killing the Aztec Emperor and about 1/3-1/2 of all the inhabitants of the valley of Mexico. (Hundreds of thousands, or maybe more than a million people, but not intentionally by the Conquistadores - in fact they were probably totally unaware that they had transmitted this disease).

The fall of Tenochtitlan was a bloody battle. The besieging Spanish had witnessed 70 of their captured comrades sacrificed by having their hearts cut out on the city's pyramids, and they were in no mood for mercy. Undoubtedly thousands of Aztecs were killed.

All in all, people intentionally killed by the Conquistadores in the conquest of Mexico was probably around 10,000? Maybe another 10,000 or so killed by the allies?

After all, there were only about a maximum of 1000 Spanish involved at any one time. So few soldiers can only kill so many.

The other major conquest by the Spanish was of Peru. Pizarro invaded Peru with 106 infantry and 62 cavalry. Pizza met the Inca to parley, and launched a surprise attack, known as the Battle of Cajamarca, which killed 2000 incas, 5 Spaniards, and captured the Inca.

Having deprived the Incas of leadership, Pizarro did not need to fight any more major battles until re-enforcements could arrive. Later, there were various battles, and the sieges of Quito and Cuzco. It took 40 years to finally pacify Peru. In all these battles, however, Inca casualties were probably less than 10,000.

The Spanish conquest of Peru was facilitated by the Incas having experienced the first smallpox epidemic even before (just before) Pizarro arrived. (Smallpox seems to have arrived in 1528, when it killed both the Emperor and his heir, precipitating the civil war in Peru. Pizarro arrived in 1532.)

Total people intentionally killed by the Conquistadores in the conquest of Peru was probably less than 10,000 people.

These were the two largest conquests in the Spanish New World. Of course, there were others, in the West Indies, the rest of South and Central America, but, if we just look at the 1500s, the number of people killed in battle (or massacres) by the Conquistadores was probably somewhere around 30,000? Add to that some murders and judicial killings. Not so many as one might think.

It was the Columbian exchange of disease which hammered the population of the Americas. Lovell estimates that by 1600 the population of the Central Andes had declined by 93% from the population of 1500. (Estimating populations declines is extremely difficult, and more difficult for the Incas than for the Aztecs because we have fewer written records.)

Source: George Lovell, "Heavy Shadows and Black Night: Disease and Depopulation in Colonial Spanish America" 1992

It's essentially impossible to give an exact number.

In my neck of the woods (Nova Scotia) there were actual bounties levied on Native scalps, each of which earned a reward when presented to the provincial government (this was set up by Edward Cornwallis, then governor of Nova Scotia).

Additionally, it is difficult to separate those "killed by plague" from those killed in a "planned genocide". Small pox laden blankets (for example) were distributed among Native populations intentionally, so in this case there is no difference between dying by plague or by intentional introduction of plagues as a facet of genocide.

While I cannot speak for all Native American or First Nations groups, I can provide a wealth of information concerning the Mi'kmaq people and these issues if so desired.