People’s preferences regarding their neighborhood environment can vary depending on their socioeconomic status and the cities where they live. This study aims to discern the relationship between neighborhood environment factors and single-family detached house sales by sale price and by central and noncentral cities. We analyzed sale prices in the Tokyo Metropolitan Area from 2015 to 2020. The neighborhood environment was assessed using flood/sediment risk and neighborhood walkability measured by net residential density, intersection density, and facility density (walking opportunity). Flood and sediment risk is a major concern that restricts the available land and is included as a negative aspect of the neighborhood environment, taking the topographic features into consideration. A comparison of the results showed that the preference for neighborhood walkability varies by socioeconomic status as well as by target cities. For most facility types, the number of walking opportunities within walking distance from houses was found to be positively related to the sale price of single-family detached houses in all quantiles. The relationship of house price with population and intersection density was found to vary depending on the price level, with a negative relationship with the sale price of relatively more expensive houses being exhibited. People who considered buying houses with relatively higher sale prices were found to devalue houses located in flood/sediment-hazardous areas more. However, it was also found that the negative relationship was slightly mitigated in the highest quantile of sale prices for houses in areas with a moderate flood risk (maximum flooding depth: 3–5 m). Plains near rivers with amenities offer high walkability but pose a flood risk, resulting in a trade-off between flood risk and neighborhood walkability. The findings suggest the use of indices representing diverse preferences in accordance with the target socioeconomic status when policymakers assess the neighborhood environment.