5356 will have higher strength on 6000 series product of that thickness.
Not all 6061 is extruded, it is likely rolled plate if it is a fully machined part.
No matter what you do, the welded part will not have anywhere near the strength of the base metal (neither yield nor ultimate tensile). You could have the part post weld heat treated and quenched, but it is quite expensive and has a relatively high distortion risk.
You may want to inquire about chamfering the hole prior to welding as it may be difficult to get complete penetration with a cylindrical hole that is that small.
You can use a copper backer if you wish to lessen the backside dropout.