It isn’t surprising that when asked to choose between a 48 star US flag or a 49 star US flag, invariably the 48 star flag is always chosen first. The reasoning is that the 48 star flag is older than the 49 star one and hence more collectible. The short answer is yes and no.
It is true that the 48 star US flag is older having been adopted officially on July, 1912 to recognize the admission of Arizona and New Mexico as the 47th and 48th states to the Union. It is the second oldest flag in years of service after the 50 star flag adopted on July 4th, 1960 to recognize the admission of Alaska and Hawaii.
The 49 star flag, however, existed only for one year. It was known that Alaska would be admitted in 1959 and flag companies rushed to produce a new 49 star pattern. However, Congress decided the next year to admit Hawaii and the 50 star pattern was made official.
So, to answer the question which is a better flag to collect? The short answer would be the 49 star flag since fewer were ever produced.
But to collect 48 star flags becomes a little trickier. Production of 48 star flags can be divided into two periods, before World War II and after World War II. Prior to WWII, most flags were made of wool and some of heavy cotton. The war effort, though, required wool for uniforms and flags were then produced using mostly heavy cotton. The best 48 star flag to collect, then, would be a wool one.
However, the star pattern matters, too. The 48 star pattern was a box pattern, all stars in a row forming a box in the canton (the blue part). If a 48 star flag has any other pattern except the box pattern, it is more desirable to collectors no matter the size. Consider that when searching for old flags.
Remember, on July 4th your local VFW, Boy Scout, fire engine company and other patriotic organizations routinely burn unserviceable old American flags. Under the Flag Code, that is the only proper way to dispose of an American flag. Consider showing up a week or two before the event to sift through the donated flags to determine if there are 48 or 49 star flags that can be sold to collectors to benefit the organization.